triangulation + clustering

.gitignore

@@ -2,4 +2,9 @@
 *egg-info
 *zip
 *log
-*in
+*in
+*sh
+*dat
+*out
+*top
+*in

CPET/source/cluster.py

@@ -470,4 +470,4 @@ def cluster_analyze(self):
                 plt.show()
         if self.plot_dwell_times == True:
             print(0)
-        return compressed_dictionary
+        return compressed_dictionary

CPET/source/pca.py

@@ -38,13 +38,17 @@ def __init__(self, options):
         else:
             self.pca_obj = None
 
-        # load dataset and metadata
-        self.field_file_list = []
-        for file in glob(self.inputpath + "/*.dat"):
-            self.field_file_list.append(file)
-        if len(self.field_file_list) == 0:
-            raise ValueError("No data found in the input path!")
-
+        # user should also be able to specify list of files alternatively 
+        if "field_file_list" not in options:
+            # load dataset and metadata
+            self.field_file_list = []
+            for file in glob(self.inputpath + "/*.dat"):
+                self.field_file_list.append(file)
+            if len(self.field_file_list) == 0:
+                raise ValueError("No data found in the input path!")
+        else:
+            self.field_file_list = options["field_file_list"]
+
         self.load()
 
     def load(self):

CPET/utils/calculator.py

@@ -754,8 +754,14 @@ def make_histograms_mem(topo_files, output_dir, plot=False):
             for line in topology_data:
                 if line.startswith("#"):
                     continue
-
-                line = line.split()
+                # strip the line of any leading or trailing whitespace
+                line = line.strip()
+                # if the line has a comma split by comma
+                if "," in line:
+                    line = line.split(",")
+                else:
+                    line = line.split()
+                #print(line)
                 distances.append(float(line[0]))
                 curvatures.append(float(line[1]))
         # print(max(distances),max(curvatures))